Found this blog post at JCVI
Are your carrying out large scale metagenomics analyses to identify differences among multiple sample sites? Are you looking for suitable analysis tools?
If you have not yet found the right analysis tool, you may be interested in the latest beta version of JCVI Metagenomics Reports (METAREP) [Test It].
METAREP is a new open source tool developed for high-performance comparative metagenomics .
It provides a suite of web based tools to help scientists view, query, browse, and compare metagenomics annotation data derived from ORFs called on metagenomics reads or assemblies.